Just to get the facts straight. What was the Dealers 'Offcial' writeup of the damage to the JK?
Why? Here's a pic of the JK intake (from my JK - I have an AEM system with an Outerwears prefilter):
The water would have to come in, go down the intake tube, then back up and through the filter (while not draining out the holes in the intake). If the OP submerged the JK then 'maybe' but.....somehow I don't thing we're getting the whole story.
Andy
Why? Here's a pic of the JK intake (from my JK - I have an AEM system with an Outerwears prefilter):

The water would have to come in, go down the intake tube, then back up and through the filter (while not draining out the holes in the intake). If the OP submerged the JK then 'maybe' but.....somehow I don't thing we're getting the whole story.
Andy